* Kid's reaction after [[spoiler:Serge helps her out of Lucca's burning orphanage]] and they watch the scene from afar. That Serge [[spoiler:vanishes ''very'' shortly after Kid laments that she will be left all on her own]] doesn't help much. Not to mention [[spoiler: the implied fates of the ''Trigger'' crew]], [[spoiler: Kid's reading of Lucca's letter]], and a number of subplots and character backstories. This can be a depressing game.
* The fight with [[spoiler: Miguel]], and the events leading up to it, especially with [[https://www.youtube.com/watch?v=UpnRWYutQy8 the music that accompanies it]], fittingly enough called "Prisoners of Fate". And then it's revealed that he's [[spoiler: Leena's]] DisappearedDad, too.
* The ending, [[spoiler: where Kid sadly declares that she'll always search for Serge, and the credits reveal that she's in our world, doing just that.]] The music just makes that scene.
* If, on a NewGamePlus, you defeat the Time Devourer before assaulting Terra Tower, then [[spoiler:the Dragon God joins forces with the demi-humans and the dwarves and slaughters the humans of El Nido. [[CallBack And Harle leaves flowers on Serge's grave on Cape Howl. Bellflowers.]]]]
* Bring Karsh to visit Home-World Zappa. Prepare to weep.
* Harle's characterization by the end of the game is a far cry from the flirtatious, seemingly uncaring jester she first appears as. Apparently, she even [[spoiler:helped Lynx burn down Lucca's orphanage]]. However, as the game goes on, Harle begins to [[CharacterDevelopment change]], especially after [[spoiler:Serge and Lynx switch bodies]]. Harle's [[VillainessesWantHeroes flirting with Serge]] turns into genuine feelings, which directly conflict with her true mission: [[spoiler:she's actually a seventh, [[TragicMonster hidden Dragon]], and therefore trying to get the Frozen Flame for the Dragon God]]. She eventually [[HeelFaceDoorSlam becomes so reluctant]] to carry out her mission, she [[MyGodWhatHaveIDone breaks down crying]] and disappears. Harle's last real appearance in the game has her being forced to carry out her mission, but at the same time begging Kid not to drag [[IWantMyBelovedToBeHappy Serge]] and the other characters down with her. When this doesn't work, Harle gives Serge one last goodbye, and then goes to [[spoiler:merge with the Dragon God]].
* Rosetta's death, [[VideoGameCrueltyPotential if you allow it to happen]].
* The talk you overhear between Doc and Orlha while Kid is poisoned and he laments he can't save her is both this and a CrowningMomentOfHeartwarming, again helped by the music in question. It becomes just a TearJerker during the scene when you take Orlha to Home World [[spoiler:and she gets to visit her dying twin sister Tia during her last moments]].
* What happens if you take Draggy to Fossil Valley: [[spoiler: He finally meets his mother... as a skeleton.]]
* When visiting Home World [[spoiler: after Serge's body is stolen]], you can meet and recruit the Home version of Zappa the blacksmith. However, in this world, Zappa is closing up shop -- the strain of the Porre occupation of Termina, plus the disappearance of his son (Karsh) was too much for him. What makes this sadder is [[spoiler: Karsh perished in the Dead Sea 3 years prior, and his parents don't know what became of him]]...but the player can lighten their burden by [[spoiler: [[HeartwarmingMoments reuniting them with Karsh's Alternate World equivalent]]]].
* The [[https://www.youtube.com/watch?v=1ZG8rPzR5ds Game Over Screen]], It tells you of how Serge is never born in the world. It's not just the screen, [[https://www.youtube.com/watch?v=xXssq6Hff8A BUT ALSO THE MUSIC]]